[English] 日本語
Yorodumi
- PDB-6b8a: Crystal structure of MvfR ligand binding domain in complex with M64 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b8a
TitleCrystal structure of MvfR ligand binding domain in complex with M64
ComponentsDNA-binding transcriptional regulator
KeywordsTRANSCRIPTION / MVFR TRANSCRIPTIONAL REGULATOR / PQSR
Function / homology
Function and homology information


regulation of transmembrane transport / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / extracellular region / plasma membrane
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #290 / : / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...D-Maltodextrin-Binding Protein; domain 2 - #290 / : / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CZG / COBALT HEXAMMINE(III) / DNA-binding transcriptional regulator / Multiple virulence factor regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKitao, T. / Steinbacher, S. / Maskos, K. / Blaesse, M. / Rahme, L.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI105902 and AI063433 United States
CitationJournal: MBio / Year: 2018
Title: Molecular Insights into Function and Competitive Inhibition ofPseudomonas aeruginosaMultiple Virulence Factor Regulator.
Authors: Kitao, T. / Lepine, F. / Babloudi, S. / Walte, F. / Steinbacher, S. / Maskos, K. / Blaesse, M. / Negri, M. / Pucci, M. / Zahler, B. / Felici, A. / Rahme, L.G.
History
DepositionOct 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding transcriptional regulator
B: DNA-binding transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7136
Polymers45,5502
Non-polymers1,1634
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-5 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.556, 121.524, 112.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein DNA-binding transcriptional regulator / Transcriptional regulator / Transcriptional regulator MvfR


Mass: 22774.854 Da / Num. of mol.: 2 / Fragment: COINDUCER BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: mvfR, AO964_20870, AOY09_01875, B0B20_09895, PAERUG_E15_London_28_01_14_10887, PAERUG_P32_London_17_VIM_2_10_11_05492, PAMH19_4335
Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZLE6, UniProt: Q9I4X0*PLUS
#2: Chemical ChemComp-CZG / 2-[(5-nitro-1H-benzimidazol-2-yl)sulfanyl]-N-(4-phenoxyphenyl)acetamide


Mass: 420.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H16N4O4S
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 31% MPD, 90 mM imidazole pH 8.0, 180mM MgCl2, 10mM Co(NH3)6Cl3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→81.78 Å / Num. obs: 21542 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.46
Reflection shellResolution: 2.65→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 4980 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0005refinement
REFMAC5.2.0005phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JVD

4jvd


Resolution: 2.65→81.78 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 21.897 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.273 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25113 863 4 %RANDOM
Rwork0.21637 ---
obs0.2178 20678 96.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 85.283 Å2
Baniso -1Baniso -2Baniso -3
1-4.34 Å20 Å20 Å2
2--2.16 Å20 Å2
3----6.5 Å2
Refinement stepCycle: LAST / Resolution: 2.65→81.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 74 17 3286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223333
X-RAY DIFFRACTIONr_bond_other_d0.0020.023042
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9954540
X-RAY DIFFRACTIONr_angle_other_deg0.9437030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33123.506154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22415551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6451528
X-RAY DIFFRACTIONr_chiral_restr0.0710.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02703
X-RAY DIFFRACTIONr_nbd_refined0.170.2561
X-RAY DIFFRACTIONr_nbd_other0.1360.22904
X-RAY DIFFRACTIONr_nbtor_refined0.160.21571
X-RAY DIFFRACTIONr_nbtor_other0.0770.22001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.89622602
X-RAY DIFFRACTIONr_mcbond_other0.3082816
X-RAY DIFFRACTIONr_mcangle_it2.40933271
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.45241522
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.98261263
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.653→2.722 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.531 57 -
Rwork0.447 1477 -
obs--94.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.67071.3211-0.33165.39810.73985.4644-0.0112-0.108-0.13550.3145-0.1206-0.76150.11420.76010.1317-0.17850.0664-0.0149-0.00170.09950.049534.719-10.1977.643
25.43921.3181-0.40685.05890.8776.3321-0.37750.3667-0.3162-0.66670.1595-0.09670.4973-0.15680.2180.04670.0760.1019-0.0212-0.01750.038219.606-25.88-4.806
35.98613.57540.81234.7535-1.78296.9220.03530.33290.02890.11050.03130.50230.3098-0.754-0.0665-0.00370.0740.07550.05870.01270.06597.39-31.11718.25
44.27020.46221.36286.8567-1.70915.55880.1472-0.3932-0.13890.8999-0.3415-0.2968-0.34310.46680.19440.06170.0292-0.0269-0.01840.08430.019927.638-22.67729.873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A93 - 166
2X-RAY DIFFRACTION1A265 - 295
3X-RAY DIFFRACTION2A167 - 264
4X-RAY DIFFRACTION3B94 - 166
5X-RAY DIFFRACTION3B265 - 295
6X-RAY DIFFRACTION4B167 - 264

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more